Structure of PDB 4xls Chain J

Receptor sequence

>4xlsJ (length=1367) Species: 271 (Thermus aquaticus)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQ
LLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDG
VALYRFPRRVRVDYLTEPKDYKVAPHMNVIVPEGAKVQAGEKIVAAIDPE
EEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADG
GKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLE
RELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDL
RPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRML
QEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVD
YSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR
RMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQ
SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPAS
GEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALN
APIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLE
TSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGM
EKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQI
EQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMA
QSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISS
HGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQ
MDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFL
IKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVV
AAESIGEPGTQLTMTQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGED
RLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEA
KGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR
LLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAA
SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVD
QRTLKAIEEARKEAVEA

3D structure

• PDB: 4xls CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
• Chain: J
• Resolution: 4.01 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	J	C1112 C1194 C1201 C1204	C988 C1070 C1077 C1080
BS02	ZN	J	C58 C73	C57 C72
BS03	MG	J	D739 D741 D743	D615 D617 D619

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:4xls, PDBe:4xls, PDBj:4xls
• PDBsum: 4xls
• PubMed: 26349034
• UniProt: Q9KWU6|RPOC_THEAQ DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)